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FASIMU specifications


Unique identifier OMICS_05179
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes


No version available

Publication for FASIMU

FASIMU citations


Model driven discovery of long chain fatty acid metabolic reprogramming in heterogeneous prostate cancer cells

PLoS Comput Biol
PMCID: 5766231
PMID: 29293497
DOI: 10.1371/journal.pcbi.1005914

[…] is considered to carry a significant metabolic flux. As is defined in [] we gave to Ɛ a value of 1. Once the thresholds were fixed, we performed the expression-based activity prediction analysis with Fasimu software by applying “compute-FBA–xs” option (See Fasimu tutorial []). […]


PFA toolbox: a MATLAB tool for Metabolic Flux Analysis

BMC Syst Biol
PMCID: 4940746
PMID: 27401090
DOI: 10.1186/s12918-016-0284-1

[…] CB, constraint-based model; COBRA, Constraint-Based Reconstruction and Analysis; FASIMU, Flux-balance Analysis based Simulations; GLPK, GNU Linear Programming kit; GUI, Graphical User Interface; IBM ILOG CPLEX, High-performance mathematical programming solver for linear programmin […]


Improving Collaboration by Standardization Efforts in Systems Biology

Front Bioeng Biotechnol
PMCID: 4259112
PMID: 25538939
DOI: 10.3389/fbioe.2014.00061

[…] d model building and simulation, which can calculate steady-state solutions for complex enzyme reactions and even solve ODE and DAE systems with delays and events. Further important tools for FBA are FASIMU (Hoppe et al., ), the VANTED (Junker et al., ) plug-in FBA-SimVis (Grafahrend-Belau et al., ), and PySCeS (Olivier et al., ). […]


Flux Balance Analysis of Cyanobacterial Metabolism: The Metabolic Network of Synechocystis sp. PCC 6803

PLoS Comput Biol
PMCID: 3699288
PMID: 23843751
DOI: 10.1371/journal.pcbi.1003081

[…] Given the constraints and conditions defined above, a solution for the flux-optimization problem was obtained using the COBRA toolbox and verified using FASIMU , both giving identical results. The reference solution under constant light is not unique. A graphical overview is given in . Overall, the solution is in good agreement with previous studies , […]


Precise generation of systems biology models from KEGG pathways

BMC Syst Biol
PMCID: 3623889
PMID: 23433509
DOI: 10.1186/1752-0509-7-15

[…] []. These formats can be used with graphical modeling applications (e.g., CellDesigner [] or Cytoscape []), complemented with rate laws (e.g., SBMLsqueezer []), used for flux balance analysis (e.g., FASIMU []), and many more applications. Therefore, converters exist that perform mostly basic conversions from KGML to those formats [-]. The drawback of many of those converters is that even for crea […]


Metabolic Consequences of TGFβ Stimulation in Cultured Primary Mouse Hepatocytes Screened from Transcript Data with ModeScore

PMCID: 3901234
PMID: 24957771
DOI: 10.3390/metabo2040983

[…] Metabolism is represented by a modified version of HepatoNet1 [] (see and ) and 987 reference functions (see and ) for which flux distributions have been computed using FASIMU [], see . In the ModeScore method ([], see also ) a regulation amplitude for each reference flux distribution and each pair of transcript profiles is computed. This value is compatible to the c […]


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FASIMU institution(s)
Institute of Biochemistry, University Medicine Charité Berlin, Berlin, Germany

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